A Protocol for Generating and Exchanging (Genome-Scale) Metabolic Resource Allocation Models

In this article, we present a protocol for generating a complete (genome-scale) metabolic resource allocation model, as well as a proposal for how to represent such models in the systems biology markup language (SBML). Such models are used to investigate enzyme levels and achievable growth rates in...

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Bibliographic Details
Published in:Metabolites 2017-09, Vol.7 (3), p.47
Main Authors: Reimers, Alexandra-M, Lindhorst, Henning, Waldherr, Steffen
Format: Article
Language:English
Subjects:
Constraint modelling
constraint-based modeling
Genomes
Growth rate
Metabolic networks
Metabolism
optimality
Protein biosynthesis
Resource allocation
SBML
Scale (ratio)
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Summary:In this article, we present a protocol for generating a complete (genome-scale) metabolic resource allocation model, as well as a proposal for how to represent such models in the systems biology markup language (SBML). Such models are used to investigate enzyme levels and achievable growth rates in large-scale metabolic networks. Although the idea of metabolic resource allocation studies has been present in the field of systems biology for some years, no guidelines for generating such a model have been published up to now. This paper presents step-by-step instructions for building a (dynamic) resource allocation model, starting with prerequisites such as a genome-scale metabolic reconstruction, through building protein and noncatalytic biomass synthesis reactions and assigning turnover rates for each reaction. In addition, we explain how one can use SBML level 3 in combination with the flux balance constraints and our resource allocation modeling annotation to represent such models.
ISSN:2218-1989
2218-1989
DOI:10.3390/metabo7030047